Variant report

Variant	rs10878089
Chromosome Location	chr12:40486605-40486606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40480723..40487168-chr12:40489659..40495663,7	K562	blood:
2	chr12:40459470..40461865-chr12:40485100..40487322,2	MCF-7	breast:
3	chr12:40481016..40484666-chr12:40485206..40488003,4	K562	blood:
4	chr12:40427544..40429854-chr12:40484526..40486904,2	MCF-7	breast:
5	chr12:40483377..40487149-chr12:40498015..40500549,4	K562	blood:
6	chr12:40484990..40487793-chr12:40489552..40494427,5	K562	blood:
7	chr12:40485743..40487373-chr12:40492578..40494956,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1005956	0.91[JPT][hapmap]
rs1031996	0.90[MEX][hapmap]
rs10506140	0.91[JPT][hapmap]
rs10747971	0.84[JPT][hapmap]
rs10784338	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs10784353	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10784356	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10784359	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784369	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877891	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10877990	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs10878031	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10878049	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174609	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11174809	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11174812	0.90[ASN][1000 genomes]
rs11174813	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11175024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12813098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823555	0.88[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1463719	0.90[MEX][hapmap]
rs1472118	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1482281	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs1586038	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1600866	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1813122	0.84[JPT][hapmap]
rs2128275	0.88[ASN][1000 genomes]
rs2128277	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2404352	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638245	0.90[MEX][hapmap]
rs2638266	0.82[CEU][hapmap]
rs2896825	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2896905	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3925535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4625545	0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4767960	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768200	0.90[JPT][hapmap]
rs4768204	0.91[JPT][hapmap]
rs530602	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs550669	0.84[JPT][hapmap]
rs555740	0.84[JPT][hapmap]
rs6581504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650226	0.84[JPT][hapmap]
rs7139216	0.85[ASN][1000 genomes]
rs716268	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313209	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs7313231	0.93[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7953129	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7959498	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs7960662	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7964150	0.84[JPT][hapmap]
rs7970812	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs878010	0.90[MEX][hapmap]
rs900253	0.85[MEX][hapmap]
rs9669240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10878089	LRRK2	cis	cerebellum	SCAN
rs10878089	ZCRB1	cis	parietal	SCAN
rs10878089	LRRK2	cis	parietal	SCAN
rs10878089	AC079630.2	cis	Esophagus Mucosa	GTEx
rs10878089	SLC2A13	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40453800-40487400	Weak transcription	Left Ventricle	heart
2	chr12:40464400-40493200	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:40474400-40497000	Weak transcription	Ovary	ovary
6	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:40475600-40496400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:40476400-40492400	Weak transcription	K562	blood
9	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:40476600-40492600	Weak transcription	Lung	lung
11	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
12	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:40477000-40492000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:40477000-40497000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:40477200-40495200	Weak transcription	Hela-S3	cervix
16	chr12:40477400-40496800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:40478600-40492600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:40479000-40493400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:40479200-40493200	Weak transcription	Fetal Heart	heart
20	chr12:40480200-40493400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:40480600-40496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:40481200-40492800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:40482000-40497800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:40482400-40493400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:40485000-40492600	Weak transcription	Fetal Intestine Large	intestine
26	chr12:40485400-40487000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:40485600-40496800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:40485800-40487800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:40486000-40492600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:40486200-40486800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr12:40486200-40488400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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